nf-core/mhcquant
Identify and quantify MHC eluted peptides from mass spectrometry raw data
1.6.0). The latest
stable release is
3.0.0
.
Define where the pipeline should find input data and save output data.
Input raw / mzML files listed in a tsv file (see help for details)
stringUse this to specify a sample sheet table including your input raw or mzml files as well as their metainformation such as SampleID and Condition. For example:
| ID | Sample | Condition | ReplicateFileName |
|---|---|---|---|
| 1 | MM15_Melanom | A | data/MM15_Melanom_W_1_A_standard.raw |
| 2 | MM15_Melanom | B | data/MM15_Melanom_W_1_B_standard.raw |
| 3 | MM17_Melanom | B | data/MM17_Melanom_W_1_B_standard.raw |
--input 'path/samples.tsv'
The output directory where the results will be saved.
string./resultsEmail address for completion summary.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (~/.nextflow/config) then you don't need to specify this on the command line for every run.
Input FASTA protein database
stringIf you have no genome reference available, the pipeline can build one using a FASTA file. This requires additional time and resources, so it's better to use a pre-build index if possible.
Set depending on whether variants should be translated to proteins and included into your fasta for database search.
booleanSet depending on whether own decoy database should be used
booleanIf you want to use your own decoys, you can specify a databaset that includes decoy sequences. However, each database entry should keep the prefix 'DECOY_'. One should consider though that this option will then prevent to append variants to the database and if not using reversed decoys the subset refinement FDR option will not work.
If one ms level in the raw ms data is not centroided, specify the level here. (eg. 2)
integer2Choose whether the specified ms_level in pick_ms_levels is centroided or not.
booleanSpecify the minimum length of peptides considered after processing
integer8Specify the maximum length of peptides considered after processing
integer12Specify the fragment mass tolerance used for the comet database search.
number0.02For High-Resolution instruments a fragment mass tolerance value of 0.02 is recommended. (See the Comet parameter documentation: eg. 0.02)
Specify the precursor mass tolerance used for the comet database search.
integer5For High-Resolution instruments a precursor mass tolerance value of 5ppm is recommended. (eg. 5)
Specify the fragment bin offset used for the comet database search.
integerFor High-Resolution instruments a fragment bin offset of 0 is recommended. (See the Comet parameter documentation: eg. 0)
Specify the maximum number of modifications that should be contained in a peptide sequence match.
integer3Specify the number of hits that should be reported for each spectrum.
integer1Specify the mass range that peptides should fullfill to be considered for peptide spectrum matching.
string800:2500Specifiy the precursor charge range that peptides should fullfill to be considered for peptide spectrum matching.
string2:3Specify which fragmentation method was used in the MS acquisition
stringSpecify which enzymatic restriction should be applied
stringunspecific cleavagefor HLA peptides rarely other enzymes are used, however most enzymes such as for example 'Trypsin' are available (see OpenMS enzymes)
Set a maximum retention time shift for the linear rt alignment
integer300Specify which fixed modifications should be applied to the database search
stringe.g. 'Carbamidomethyl (C)' (see OpenMS modifications)
Specify which variable modifications should be applied to the database search
stringOxidation (M)e.g. 'Oxidation (M)' (see OpenMS modifications)
Include x ions into the peptide spectrum matching
booleanInclude z ions into the peptide spectrum matching
booleanInclude a ions into the peptide spectrum matching
booleanInclude c ions into the peptide spectrum matching
booleanInclude NL ions into the peptide spectrum matching
booleanInclude precursor ions into the peptide spectrum matching
booleantrueSize of Spectrum batch for Comet processing (Decrease/Increase depending on Memory Availability)
integer500Specify a .tsv file containing the information about genomic variants (vcf files < v.4.2) for each sample.
string| Sample | VCF_FileName |
|---|---|
| MM15_Melanom | data/MM15_variants.vcf |
| MM17_Melanom | data/MM17_variants.vcf |
Specify the level at which the false discovery rate should be computed.
stringSpecify the false discovery rate threshold at which peptide hits should be selected.
number0.01Set if MHCquant should be run in SubsetFDR mode
booleanSubsetFDR makes use of binding predictions applying the tool mhcflurry to subset all PSMs not passing the q-value threshold. If specified the FDR will be refined using Percolator on the subset of predicted binders among all PSMs resulting in an increased identification rate. (Please be aware that this option is only available for MHC class I data of alleles that are supported by mhcflurry)
Affinity threshold (nM) used to define binders for PSM subset selection in the FDR refinement procedure
integer500Specify percolator descriptor feature set
integerSee percolator description (https://github.com/percolator/percolator/wiki/Retention-time-and-calibration)
Use klammer retention time features for Percolator rescoring
booleanMaximum subset for percolator training iterations
integerSkip quantification and only yield peptide identifications
booleanCompute FDR for the targeted approach
string(Weisser H. and Choudhary J.S. J Proteome Res. 2017 Aug 4)
Specify a cut off probability value for quantification events as a filter
numberSpecify a .tsv file containing the MHC alleles of your probes as well as their metadata such as SampleID.
string| Sample | HLA_Alleles_Class_1 | HLA_Alleles_Class_2 |
|---|---|---|
| MM15_Melanom | A* 03:01;A* 68:01;B* 27:05;B* 35:03;C* 02:02;C* 04:01 | HLA-DRB1* 01:01;HLA-DQB1* 03:19;HLA-DQA1* 05:01 |
| MM17_Melanom | A* 02:01;B* 07:01;B* 26:01;C* 11:01;C* 01:01 | HLA-DRB1* 01:02;HLA-DRB3* 02:02;HLA-DRB4* 01:03 |
Set flag depending on whether MHC class 1 binding predictions using the tool mhcflurry should be run.
booleanSet flag depending on whether MHC class 2 binding predictions using the tool mhcnuggets should be run.
booleanSpecify genomic reference used for variant annotation
stringSpecify style of tool used for variant annotation - currently supported
stringSpecify whether insertions and deletions should not be considered for variant translation
booleantrueSpecify whether frameshifts should not be considered for variant translation
booleantrueSpecify whether snps should not be considered for variant translation
booleanSet this option to predict retention times of all identified peptides and possible neoepitopes based on high scoring ids
booleanLess common options for the pipeline, typically set in a config file.
Display help text.
booleanMethod used to save pipeline results to output directory.
stringThe Nextflow publishDir option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See Nextflow docs for details.
Workflow name.
stringA custom name for the pipeline run. Unlike the core nextflow -name option with one hyphen this parameter can be reused multiple times, for example if using -resume. Passed through to steps such as MultiQC and used for things like report filenames and titles.
Email address for completion summary, only when pipeline fails.
string^([a-zA-Z0-9_\-\.]+)@([a-zA-Z0-9_\-\.]+)\.([a-zA-Z]{2,5})$This works exactly as with --email, except emails are only sent if the workflow is not successful.
Send plain-text email instead of HTML.
booleanSet to receive plain-text e-mails instead of HTML formatted.
Do not use coloured log outputs.
booleanSet to disable colourful command line output and live life in monochrome.
Directory to keep pipeline Nextflow logs and reports.
string${params.outdir}/pipeline_infoOptions for the reference genome indices used to align reads.
Do not load the iGenomes reference config.
booleanDo not load igenomes.config when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in igenomes.config.
Set the top limit for requested resources for any single job.
Maximum number of CPUs that can be requested for any single job.
integer16Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. --max_cpus 1
Maximum amount of memory that can be requested for any single job.
string128.GBUse to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. --max_memory '8.GB'
Maximum amount of time that can be requested for any single job.
string240.hUse to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. --max_time '2.h'
Parameters used to describe centralised config profiles. These should not be edited.
Git commit id for Institutional configs.
stringmasterProvide git commit id for custom Institutional configs hosted at nf-core/configs. This was implemented for reproducibility purposes. Default: master.
## Download and use config file with following git commit id
--custom_config_version d52db660777c4bf36546ddb188ec530c3ada1b96
Base directory for Institutional configs.
stringhttps://raw.githubusercontent.com/nf-core/configs/masterIf you're running offline, nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell nextflow where to find them with the custom_config_base option. For example:
## Download and unzip the config files
cd /path/to/my/configs
wget https://github.com/nf-core/configs/archive/master.zip
unzip master.zip
## Run the pipeline
cd /path/to/my/data
nextflow run /path/to/pipeline/ --custom_config_base /path/to/my/configs/configs-master/
Note that the nf-core/tools helper package has a
downloadcommand to download all required pipeline files + singularity containers + institutional configs in one go for you, to make this process easier.
Institutional configs hostname.
stringInstitutional config description.
stringInstitutional config contact information.
stringInstitutional config URL link.
string